lh12565

Thanks, when I add `output_values = True`, I find the value of `rank_acceleration` or `rank_abs_acceleration` are different, see below, so the sorting is inconsistent for me. I don't know if...

> Hi @Xiaojieqiu , when I used dyn.tl.gene_wise_confidence, I found only 2000 genes had been evaluated. But my anndata still have 30000~ genes, I guess it's already filtered at dyn.pp.recipe_monocle...

Hi, @Xiaojieqiu yes, I use cscRNA-seq datasets. I have run `dyn.pp.recipe_monocle(adata)` before run `dyn.tl.gene_wise_confidence`. I didn't find `cell_wise_velocity`, did you mean `tl.cell_velocities`? When I run code as below, it seems...

Thanks a lot. I have one more question. In my research, some studies said one cancer subtype (sub1) can switch to another (sub2). And some studies said the sub2 can...

> if you find the transition is sub2->sub1 from the labeling data, then it means the transition from sub1->sub2 maybe is rare. > > However, you can always use the...

Is the meaning of attractors of lap_tutorial same as the meaning of attractors of Zebrafish pigmentation's tutorial? Both represent terminal cells? If yes, HSC should have no attractor, (HSC seems...

> the cell type to color map is this: `c=("black" if cur_ftype == -1 else "blue" if cur_ftype == 0 else "red"),` see this line of code > > https://github.com/aristoteleo/dynamo-release/blob/de6c6e737fb10177ff97fbb8179a1b0139c836d2/dynamo/plot/topography.py#L390...

Hi, @mattragoza I run the code: "python3 generate.py config/generate.config". There is also an error: ``` Setting random seed to 0 Loading data Initializing generative model Loading generative model state Initializing...

> How much GPU memory does your card have? I tried to reduce the batch size to 1, but the error is still there. My GPU memory is 32G.

> If you run the code on the CPU, it may give a more informative error message. I just pushed a commit that lets you control this by setting the...